Contacts of the helix formed by residues 298 - 313 (chain B) in PDB entry 2POD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ALA* 5.3 3.5 - - - +
81B MSE 3.7 15.6 - - - -
84B ASN* 5.2 2.5 - - - +
85B SER* 3.0 17.7 + - - -
88B ASP* 4.2 4.5 - - - +
296B TRP 3.6 0.6 - - - -
297B CYS* 1.3 78.7 - - - +
299B GLY* 1.3 63.7 + - - +
301B SER* 4.2 6.9 - - - -
302B GLU* 3.7 24.3 + - - +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 3.3 8.5 + - - -
88B ASP* 3.4 17.9 - - - -
89B ILE* 5.0 0.7 - - - -
294B ILE* 3.2 25.4 + - - -
297B CYS* 3.9 2.1 - - - -
298B GLY* 1.3 77.9 - - - +
300B LEU* 1.3 64.4 + - - -
301B SER 3.2 1.6 - - - -
303B ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ASP* 2.7 6.7 + - - -
89B ILE* 4.6 12.2 - - + +
92B TRP* 3.6 40.2 - - + +
103B ILE* 3.9 20.9 - - + -
107B LEU* 4.6 15.9 - - + -
294B ILE* 4.5 19.0 - - + +
299B GLY* 1.3 71.0 - - - -
301B SER* 1.3 54.4 + - - +
303B ALA* 4.3 3.4 - - + -
304B ARG* 2.7 39.9 + - - +
330B ALA* 3.8 35.0 - - + +
334B LEU* 4.2 19.5 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.2 23.4 + - - +
62B ASP* 4.1 4.9 + - - -
65B ALA* 4.2 13.9 - - - -
88B ASP* 2.9 29.7 + - - -
92B TRP* 3.5 2.1 + - - +
298B GLY 4.2 4.3 - - - -
300B LEU* 1.3 76.2 - - - +
302B GLU* 1.3 62.8 + - - +
304B ARG* 3.5 20.7 + - - +
305B LYS* 3.3 31.5 - - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 5.6 6.6 - - + +
274B THR* 3.9 15.1 - - + +
275B ARG* 2.9 63.3 + - - +
276B TRP* 3.9 5.3 - - - -
297B CYS 3.6 19.1 - - - +
298B GLY* 3.7 24.8 + - - +
299B GLY 3.5 2.2 + - - -
300B LEU 3.4 0.4 - - - -
301B SER* 1.3 79.7 - - - +
303B ALA* 1.3 60.3 + - - +
305B LYS* 2.9 8.9 + - - +
306B ILE* 2.9 36.0 + - + +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LEU* 3.9 14.9 - - + +
294B ILE* 3.8 21.5 - - + -
297B CYS* 3.8 15.2 - - - -
299B GLY 3.1 18.5 + - - +
300B LEU* 4.0 3.4 - - - +
302B GLU* 1.3 74.4 - - - +
304B ARG* 1.3 65.5 + - - +
306B ILE* 4.0 9.6 - - - +
307B ALA* 3.3 22.7 + - - +
334B LEU* 3.9 11.0 - - + +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.9 0.2 - - - +
62B ASP* 2.8 40.2 + - - -
92B TRP* 3.4 40.0 - - - -
107B LEU* 3.6 30.0 + - + +
300B LEU 2.7 27.1 + - - +
301B SER* 3.5 21.4 + - - +
303B ALA* 1.3 72.5 - - - +
305B LYS* 1.3 72.3 + - + +
307B ALA* 3.6 4.5 + - - +
308B SER* 3.4 23.7 + - - -
334B LEU* 4.3 10.6 - - - +
337B ASN* 5.8 4.8 + - - +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 3.2 31.4 + - - +
65B ALA* 6.2 1.0 - - - +
275B ARG* 3.6 53.4 - - - +
301B SER* 3.3 25.0 + - - +
302B GLU* 2.9 6.9 + - - +
304B ARG* 1.3 93.2 - - + +
306B ILE* 1.3 61.8 + - - +
307B ALA 3.3 0.2 - - - -
308B SER* 2.9 10.0 + - - -
309B MSE 2.9 31.8 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 3.7 23.1 - - - +
275B ARG* 4.0 13.7 - - - +
278B PHE* 3.5 52.9 - - + -
282B LEU* 5.5 1.0 - - + +
290B VAL* 4.0 8.7 - - + -
292B LEU* 3.7 32.1 - - + -
297B CYS* 4.3 2.2 - - - -
302B GLU* 2.9 30.6 + - + +
303B ALA 4.1 0.9 - - - +
305B LYS* 1.3 76.1 - - - +
307B ALA* 1.3 55.9 + - - +
309B MSE 3.3 8.7 + - - +
310B ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ALA 3.3 17.7 + - - +
304B ARG 3.6 5.8 - - - +
305B LYS 3.3 0.2 - - - -
306B ILE* 1.3 78.7 - - - +
308B SER* 1.3 61.3 + - - +
310B ALA 3.5 0.7 + - - -
311B GLU 3.2 7.3 + - - -
317B VAL* 3.7 26.0 - - + +
334B LEU* 4.5 6.7 - - + -
338B ALA* 4.3 16.8 - - + -
340B ASN* 3.0 35.2 + - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG 3.4 6.2 + - - -
305B LYS* 2.9 25.1 + - - +
307B ALA* 1.3 77.7 - - - +
309B MSE 1.3 62.5 + - - +
311B GLU* 3.7 22.1 - - - +
312B ALA* 3.7 6.8 + - - +
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Residues in contact with MSE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ARG* 4.2 36.1 - - + +
278B PHE* 5.2 2.0 - - + -
279B ARG* 4.0 23.8 - - + -
282B LEU* 3.7 24.5 - - + -
305B LYS 2.9 14.5 + - - +
306B ILE* 3.4 11.7 - - - +
308B SER* 1.3 74.3 + - - +
310B ALA* 1.3 59.4 + - - +
311B GLU 3.2 0.2 - - - -
312B ALA* 3.0 21.3 + - - +
313B TRP* 3.2 40.9 - - + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B LEU* 4.2 14.1 - - + +
290B VAL* 3.8 34.5 - - + -
306B ILE 2.9 19.5 + - - +
307B ALA 3.7 5.4 - - - +
309B MSE 1.3 72.1 - - - +
311B GLU* 1.3 59.7 - - - +
313B TRP* 3.1 7.7 + - - +
315B LEU* 2.9 30.5 + - + +
317B VAL* 4.0 3.6 - - + -
340B ASN* 3.9 9.0 - - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.2 11.7 + - - +
308B SER* 3.7 17.8 - - - +
309B MSE 3.2 0.6 - - - -
310B ALA* 1.3 74.6 - - - +
312B ALA* 1.3 57.4 + - - +
314B HIS* 2.9 25.4 + - - +
315B LEU 4.0 3.6 - - - +
339B PRO* 3.8 37.8 - - - +
340B ASN* 3.6 20.7 - - + +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER 3.7 6.3 + - - +
309B MSE 3.0 15.2 + - - +
311B GLU* 1.3 77.4 - - - +
313B TRP* 1.3 71.6 + - + +
314B HIS* 3.3 12.9 + - - -
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Residues in contact with TRP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B LEU* 3.6 56.0 + - + -
283B GLU* 5.4 6.2 - - + +
285B ASN* 4.5 11.9 + - - -
309B MSE 3.2 53.4 - - + -
310B ALA 3.1 8.9 + - - +
312B ALA* 1.3 89.3 - - + +
314B HIS* 1.3 74.0 + - - +
315B LEU* 3.2 16.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il